AMBER Archive (2004)

Subject: Re: AMBER: Trajectory file

From: Guanglei Cui (
Date: Wed Jun 09 2004 - 15:27:16 CDT

You can try ptraj and read in your reference structure, and do an rms.
In the trajectory, all structures should be superimposed

trajin ...
trajin ...
trajout ...
reference ...
rms ...


Joseph Nachman wrote:

> Hello all -
> I'm trying to make a pseudo trajectoryu file from a number of pdb files. I
> know how to combine them and output the "crd" file in Carnal, byut I
> realizr that I have to superimpose the structures. Is there a way to do
> thatin ptraj or Carnal, or do I habve to generate by hand the superimposed
> structures, before inputing them into Carnal?
> It looks as if one can use FIT in Carnal to superimpose a structure on
> reference structure, if one calculates, for instance, RMSD - but I'm not
> sure how to save the fitted structures and hopw to write them out.
> Thanks for your help,
> Joseph
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to